Hi,
Now the scripts are working. Log files are being generated successfully.
I am trying to use complete_pdb.py to add missing atoms to my pdbfile.
Here is the command i am using
mod9v5 complete_pdb.py (ChainA.pdb)
The following log file is being generated
MODELLER 9v5, 2008/10/07, r6498
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2008 Andrej Sali All Rights Reserved
Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Windows Vista build 6001 Service Pack 1, EINSTEIN, SMP, x86 Family 6 Model 14 Stepping 12
Date and time of compilation : 2008/10/07 16:19:49 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2009/01/08 00:07:19
Total CPU time [seconds] : 0.22
I have been using the following link http://salilab.org/modeller/manual/node403.html
Am i missing something.
Please help me how to use it.
Regards,
Sarath On Wed, Jan 7, 2009 at 4:28 PM, Modeller Caretaker < modeller-care@salilab.org> wrote:
> Sarath Chandra wrote: > > I am Sarath and i am an intern in Max Planck Institute of Biophysical > > Chemistry Gottingen. I am working on Molecular Dynamic simulations of > > Photosystem II a membrane protein which has 17 subunits and all of these > > subunits has all together 200 atoms missing. > > > > I am trying to use complete_pdb.py and i am facing an error "import > > site failed;" > > > > Any suggestions on a the problem and how to use the script > > See #2 at http://salilab.org/modeller/release.html#issues > > The script should still run fine, despite that warning. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
Sarath Chandra wrote: > Now the scripts are working. Log files are being generated successfully. > > I am trying to use complete_pdb.py to add missing atoms to my pdbfile. > > Here is the command i am using > > mod9v5 complete_pdb.py (ChainA.pdb)
Is that really exactly what you're typing, complete with the "(ChainA.pdb)" ? I can't tell if that will work without seeing your complete_pdb.py script, but my suspicion is that it won't if you are putting literal parentheses in there.
> The following log file is being generated ...
OK, that log file shows that Modeller is successfully running. But maybe you didn't tell it to do anything?
> I have been using the following link > http://salilab.org/modeller/manual/node403.html
That describes how to use the complete_pdb() function, but you still have to write a little script to actually use it. If all you want to do is read in an input PDB, fill in missing atoms, and write out the completed PDB, something like the following should work:
from modeller import * from modeller.scripts import complete_pdb
env = environ() env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib')
m = complete_pdb(env, "input.pdb") m.write(file="output.pdb")
Ben Webb, Modeller Caretaker
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Sarath Chandra